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They weren't actually killed; their weapons systems were stolen or copied, I believe.
If you got to the secret fight with Gorea 2/True Gorea/whatever it's name is, shortly before the fight and as Samus escapes, six multicoloured flashes of light escape the Oubliette. These are the hunters' ships escaping the blast.
Fan of Bullet Hell, Cave and Touhou mostly, and <3 Patchouli Knowledge. Playing: DeathSmiles, Castlevania: PoR, Fire Emblem 8, Rune Factory 3, Crash Bash
Those colors commonly represent the Hunters in the game, plus each other's main weapons (Battlehammer is green, Imperialist red, etc.). So it is clear those flying lights are the Hunter's ships flying away, because seriously, what else could it be? Nothing else! Specially when you see Weavel's ship when you just arrive in Oubliette.
"Behold my powers! I am the most powerful Pokemon in the world!" -Mewtwo 3DS FC: 4339-2716-5379